☰ Navigation Tabs
Crystal Structure of SARS-CoV-2 Main Protease M49I mutant in complex with Nirmatrelvir
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7MBG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M MES pH 6.7, 5% DMSO, 8% PEG 4000 Cryo protected with 40% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.6 52.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.859 α = 90 b = 100.068 β = 90 c = 103.533 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 2M 2022-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS SIRIUS BEAMLINE MANACA 0.977180 LNLS SIRIUS MANACA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.868 72.056 51.42 0.084 0.989 7.4 5.6 30317
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.868 1.937 2.37 0.377 0.684 1.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7MBG 1.868 72.056 30317 1493 51.246 0.196 0.194 0.194 0.24 0.2399 33.494
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.206 0.119 -0.325
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.833 r_dihedral_angle_3_deg 16.561 r_dihedral_angle_4_deg 16.488 r_dihedral_angle_1_deg 7.838 r_lrange_it 6.779 r_lrange_other 6.749 r_scangle_it 4.348 r_scangle_other 4.348 r_mcangle_it 3.735 r_mcangle_other 3.734
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.833 r_dihedral_angle_3_deg 16.561 r_dihedral_angle_4_deg 16.488 r_dihedral_angle_1_deg 7.838 r_lrange_it 6.779 r_lrange_other 6.749 r_scangle_it 4.348 r_scangle_other 4.348 r_mcangle_it 3.735 r_mcangle_other 3.734 r_scbond_it 2.66 r_scbond_other 2.66 r_mcbond_it 2.289 r_mcbond_other 2.288 r_angle_refined_deg 1.454 r_angle_other_deg 1.274 r_symmetry_xyhbond_nbd_refined 0.28 r_nbd_other 0.234 r_xyhbond_nbd_refined 0.214 r_nbd_refined 0.193 r_symmetry_nbd_other 0.192 r_symmetry_nbd_refined 0.168 r_nbtor_refined 0.164 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.062 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4680 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling PHASER phasing